相关论文: From DNA sequence analysis to modeling replication…
We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…
Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
Comparison of human and chimpanzee genomes has received much attention, because of paramount role for understanding evolutionary step distinguishing us from our closest living relative. In order to contribute to insight into Y chromosome…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
Stochastic rearrangement of germline DNA by VDJ recombination is at the origin of immune system diversity. This process is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions…
Understanding the evolutionary relationship among species is of fundamental importance to the biological sciences. The location of the root in any phylogenetic tree is critical as it gives an order to evolutionary events. None of the…
Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…
Motivation: Recombination rates vary considerably at the fine scale within mammalian genomes, with the majority of recombination occurring within hotspots of ~2 kb in width. We present a method for inferring the location of recombination…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
Spatial fluctuations of guanine and cytosine base content (GC%) are studied by spectral analysis for the complete set of human genomic DNA sequences. We find that (i) the 1/f^alpha decay is universally observed in the power spectra of all…
An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability relies on the existence of sufficiently large genotype networks, that is ensembles of sequences with the same phenotype that…
Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and macroscopic…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
We study the primary DNA structure of four of the most completely sequenced human chromosomes (including chromosome 19 which is the most dense in coding), using Non-extensive Statistics. We show that the exponents governing the decay of the…
Asynchronous replication of the genome has been associated with different rates of point mutation and copy number variation (CNV) in human populations. Here, we explored if the bias in the generation of CNV that is associated to DNA…
Mapping human genetic variation is fundamentally interesting in fields such as anthropology and forensic inference. At the same time patterns of genetic diversity confound efforts to determine the genetic basis of complex disease. Due to…
Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…